Jupyter "pip install" failing

srappocc · August 23, 2017, 9:24pm

Hi Danilo, All,

I’m now getting to using Jupyter with pyroot. I have a problem with the “pip install”:

sudo pip install jupyter metakernel zmq

and it gives me many successes and then an error. Any ideas? I had anaconda installed before, then removed it, and the error remains.


Collecting backports_abc>=0.4 (from tornado>=4->notebook->jupyter)
  Downloading backports_abc-0.5-py2.py3-none-any.whl
Requirement already satisfied: wcwidth in /Library/Python/2.7/site-packages (from prompt-toolkit<2.0.0,>=1.0.0->jupyter-console->jupyter)
Requirement already satisfied: scandir; python_version < "3.5" in /Library/Python/2.7/site-packages (from pathlib2; python_version == "2.7" or python_version == "3.3"->ipython<6.0.0,>=4.0.0; python_version < "3.3"->ipywidgets->jupyter)
Requirement already satisfied: functools32; python_version == "2.7" in /Library/Python/2.7/site-packages (from jsonschema!=2.5.0,>=2.4->nbformat>=4.2.0->ipywidgets->jupyter)
Collecting webencodings (from html5lib>=0.99999999->bleach->nbconvert->jupyter)
  Downloading webencodings-0.5.1-py2.py3-none-any.whl
Installing collected packages: python-dateutil, jupyter-client, singledispatch, certifi, backports-abc, tornado, ipykernel, webencodings, html5lib, bleach, nbconvert, terminado, notebook, widgetsnbextension, ipywidgets, qtconsole, jupyter-console, jupyter, metakernel, zmq
  Found existing installation: python-dateutil 1.5
    Uninstalling python-dateutil-1.5:
Exception:
Traceback (most recent call last):
  File "/Library/Python/2.7/site-packages/pip/basecommand.py", line 215, in main
    status = self.run(options, args)
  File "/Library/Python/2.7/site-packages/pip/commands/install.py", line 342, in run
    prefix=options.prefix_path,
  File "/Library/Python/2.7/site-packages/pip/req/req_set.py", line 778, in install
    requirement.uninstall(auto_confirm=True)
  File "/Library/Python/2.7/site-packages/pip/req/req_install.py", line 754, in uninstall
    paths_to_remove.remove(auto_confirm)
  File "/Library/Python/2.7/site-packages/pip/req/req_uninstall.py", line 115, in remove
    renames(path, new_path)
  File "/Library/Python/2.7/site-packages/pip/utils/__init__.py", line 267, in renames
    shutil.move(old, new)
  File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/shutil.py", line 299, in move
    copytree(src, real_dst, symlinks=True)
  File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/shutil.py", line 208, in copytree
    raise Error, errors
Error: [('/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/dateutil/__init__.py', '/tmp/pip-MhGxNG-uninstall/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/dateutil/__init__.py', "[Errno 1] Operation not permitted: '/tmp/pip-MhGxNG-uninstall/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/dateutil/__init__.py'"), ('/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/dateutil/__init__.pyc', '/tmp/pip-MhGxNG-uninstall/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/dateutil/__init__.pyc', "[Errno 1] Operation not permitted: '/tmp/pip-MhGxNG-uninstall/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/dateutil/__init__.pyc'"), ('/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/dateutil/easter.py', '/tmp/pip-MhGxNG-uninstall/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/dateutil/easter.py', "[Errno 1] Operation not permitted: '/tmp/pip-MhGxNG-uninstall/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/dateutil/easter.py'"), ('/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/dateutil/easter.pyc', '/tmp/pip-MhGxNG-uninstall/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/dateutil/easter.pyc', "[Errno 1] Operation not permitted: '/tmp/pip-MhGxNG-uninstall/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/dateutil/easter.pyc'"), ('/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/dateutil/parser.py', '/tmp/pip-MhGxNG-uninstall/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/dateutil/parser.py', "[Errno 1] Operation not permitted: '/tmp/pip-MhGxNG-uninstall/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/dateutil/parser.py'"), ('/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/dateutil/parser.pyc', '/tmp/pip-MhGxNG-uninstall/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/dateutil/parser.pyc', "[Errno 1] Operation not permitted: '/tmp/pip-MhGxNG-uninstall/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/dateutil/parser.pyc'"), ('/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/dateutil/relativedelta.py', '/tmp/pip-MhGxNG-uninstall/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/dateutil/relativedelta.py', "[Errno 1] Operation not permitted: '/tmp/pip-MhGxNG-uninstall/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/dateutil/relativedelta.py'"), ('/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/dateutil/relativedelta.pyc', '/tmp/pip-MhGxNG-uninstall/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/dateutil/relativedelta.pyc', "[Errno 1] Operation not permitted: '/tmp/pip-MhGxNG-uninstall/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/dateutil/relativedelta.pyc'"), ('/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/dateutil/rrule.py', '/tmp/pip-MhGxNG-uninstall/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/dateutil/rrule.py', "[Errno 1] Operation not permitted: '/tmp/pip-MhGxNG-uninstall/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/dateutil/rrule.py'"), ('/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/dateutil/rrule.pyc', '/tmp/pip-MhGxNG-uninstall/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/dateutil/rrule.pyc', "[Errno 1] Operation not permitted: '/tmp/pip-MhGxNG-uninstall/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/dateutil/rrule.pyc'"), ('/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/dateutil/tz.py', '/tmp/pip-MhGxNG-uninstall/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/dateutil/tz.py', "[Errno 1] Operation not permitted: '/tmp/pip-MhGxNG-uninstall/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/dateutil/tz.py'"), ('/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/dateutil/tz.pyc', '/tmp/pip-MhGxNG-uninstall/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/dateutil/tz.pyc', "[Errno 1] Operation not permitted: '/tmp/pip-MhGxNG-uninstall/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/dateutil/tz.pyc'"), ('/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/dateutil/tzwin.py', '/tmp/pip-MhGxNG-uninstall/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/dateutil/tzwin.py', "[Errno 1] Operation not permitted: '/tmp/pip-MhGxNG-uninstall/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/dateutil/tzwin.py'"), ('/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/dateutil/tzwin.pyc', '/tmp/pip-MhGxNG-uninstall/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/dateutil/tzwin.pyc', "[Errno 1] Operation not permitted: '/tmp/pip-MhGxNG-uninstall/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/dateutil/tzwin.pyc'"), ('/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/dateutil/zoneinfo/__init__.py', '/tmp/pip-MhGxNG-uninstall/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/dateutil/zoneinfo/__init__.py', "[Errno 1] Operation not permitted: '/tmp/pip-MhGxNG-uninstall/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/dateutil/zoneinfo/__init__.py'"), ('/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/dateutil/zoneinfo/__init__.pyc', '/tmp/pip-MhGxNG-uninstall/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/dateutil/zoneinfo/__init__.pyc', "[Errno 1] Operation not permitted: '/tmp/pip-MhGxNG-uninstall/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/dateutil/zoneinfo/__init__.pyc'"), ('/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/dateutil/zoneinfo/zoneinfo-2010g.tar.gz', '/tmp/pip-MhGxNG-uninstall/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/dateutil/zoneinfo/zoneinfo-2010g.tar.gz', "[Errno 1] Operation not permitted: '/tmp/pip-MhGxNG-uninstall/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/dateutil/zoneinfo/zoneinfo-2010g.tar.gz'"), ('/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/dateutil/zoneinfo', '/tmp/pip-MhGxNG-uninstall/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/dateutil/zoneinfo', "[Errno 1] Operation not permitted: '/tmp/pip-MhGxNG-uninstall/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/dateutil/zoneinfo'"), ('/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/dateutil', '/tmp/pip-MhGxNG-uninstall/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/dateutil', "[Errno 1] Operation not permitted: '/tmp/pip-MhGxNG-uninstall/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/dateutil'")]

srappocc · August 23, 2017, 11:25pm

I actually got a bit further. Apparently pip is not compatible with later versions of macOS as described here. If I do :

pip install jupyter metakernel zmq --user

the install succeeds, but then ROOT cannot create a notebook (although mostly everything else works fine):

gandalf:% root --notebook
Error executing Jupyter command 'notebook': [Errno 2] No such file or directory

srappocc · August 23, 2017, 11:54pm

This was apparently a jupyter problem with macOS. The solution was here.

Danilo · August 24, 2017, 7:03am

Hi Sal,

thanks for leaving a reference about this problem and its solution.

D

system · September 7, 2017, 7:03am

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